in the shell

I just watched the remaining episodes of 2nd GIG yesterday and I still can't pin down how the concept of a Stand Alone Complex applies to Kuze and the revolt of the refugees. I know the individual eleven are stand alones due to their actions and ideology copying and being driven by a nonexistent essay espousing a nonexistent essay, but what about Kuze/Gouda, the major and section 9? I remember Ishikawa remarking to himself in Martial Law Episode 23 that different parties: Kuze and the refugees, Gouda and the Cabinet Intelligence Agency, the chief and the major, and Ishikawa and the Tachikomas are all running their own stand alone complexes. How does this work? I don't see how they all mimic any one belief system or set of actions so much as respond to what the other do. The definition of "Stand Alone Complex" seems to have gotten too loose by this point.

You have misheard - or someone has mistranslated - what Ishikawa said. They don't have separate Stand Alone Complexes, but separate standalone strategies, which is an entirely different matter. That simply means, how well each party will perform independent from all others.

The Individual Eleven were a Stand Alone Complex, albeit a fake one and I imagine that the relationship between the refugees and Kuze is at least occasionally, one, as well - namely, in times when Kuze is gone and the refugees are doing what they imagine Kuze wants them to do.